Interpretive Summary: The compact (dwarf) plant architecture is an important trait in cucumber (Cucumis sativus L.) breeding that has the potential to be used in once-over mechanical harvest of cucumber production. Compact growth habit is controlled by a simply inherited recessive gene cp. With 150 F2:3 families derived from two inbred cucumber lines PI 308915 (compact vining) and PI 249561 (regular vining), we conducted a genome wide molecular mapping with microsatellite (simple sequence repeat, SSR) markers. A framework genetic map was constructed consisting of 187 SSR loci in seven linkage groups (chromosomes) covering 527.5 cM of genetic distances. Linkage analysis placed cp at the distal half of cucumber Chromosome 4. Cosegregating molecular markers with the compact locus were identified through whole genome scaffold-based chromosome walking. Fine genetic mapping with 1,273 F2 plants delimited the cp locus in a 220 kb genomic DNA region. Annotation and function prediction of genes in this region identified a homolog of the cytokinin oxidase (CKX) gene which may be a potential candidate of the compact locus. Alignment of the CKX gene homologs from both parental lines revealed a 3-base pair deletion in the first exon of PI 308915, which can serve as a marker for marker-assisted selection of the compact phenotype. This work also provides a solid foundation for map-based cloning of the compact gene and understanding the molecular mechanisms of the dwarfing in cucumber.

Technical Abstract:
The compact or dwarf plant architecture is an important trait in cucumber breeding. Compact cucumber has the potential to be used in once-over mechanical harvest of pickling cucumber production. Compact growth habit is controlled by a simply inherited recessive gene. To facilitate markers assisted selection of the recessively inherited dwarf gene in cucumber breeding, molecular mapping was conducted aiming to identifying markers for the compact gene. With 150 F2:3 families derived from two cucumber lines PI 308915 (compact vining) and PI 249561 (regular vining), a framework genetic map was constructed using microsatellite or SSR markers. This genetic map was composed of 188 SSR markers in seven chromosomes covering 527.5 cM of genetic distances. The compact gene was placed in the long arm of cucumber Chromosome 4. Cosegregating molecular markers with the compact gene were identified through whole genome scaffold-based chromosome walking. Fine genetic mapping with 1,273 F2 plants delimited the cp locus in a 220 kb genomic DNA region. Function prediction in this region identified the cytokinin oxidase (CKX) gene which may be a potential candidate of the compact locus. Alignment of the CKX gene homologs from both parental lines revealed a 3-base pair deletion in the CKX gene of PI 308915, which can serve as a marker for marker-assisted selection of the compact phenotype. This work also provides a solid foundation for map-based cloning of the compact gene and understanding the molecular mechanisms of the dwarfing in cucumber.